PDB-4rls: Lactate Dehydrogenase in complex with inhibitor compound 47

ID or keywords:

Entry

Database: PDB / ID: 4rls

Title

Lactate Dehydrogenase in complex with inhibitor compound 47

Components

L-lactate dehydrogenase A chain

Keywords

OXIDOREDUCTASE

Function / homology

Function and homology information

oxidoreductase complex / Pyruvate metabolism / L-lactate dehydrogenase / lactate metabolic process / L-lactate dehydrogenase activity / pyruvate metabolic process / substantia nigra development / glycolytic process / cadherin binding / mitochondrion ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.91 Å

Authors

Eigenbrot, C. / Ultsch, M.H.

Citation

Journal: Bioorg.Med.Chem.Lett. / Year: 2014
Title: Identification of 3,6-disubstituted dihydropyrones as inhibitors of human lactate dehydrogenase.
Authors: Fauber, B.P. / Dragovich, P.S. / Chen, J. / Corson, L.B. / Ding, C.Z. / Eigenbrot, C. / Labadie, S. / Malek, S. / Peterson, D. / Purkey, H.E. / Robarge, K. / Sideris, S. / Ultsch, M. / Wei, ...

History

Deposition	Oct 17, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 12, 2014	Provider: repository / Type: Initial release
Revision 1.1	Dec 24, 2014	Group: Database references
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4rls.cif.gz	532.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4rls.ent.gz	441.1 KB	Display	PDB format
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Validation report

Summary document	4rls_validation.pdf.gz	1.8 MB	Display	wwPDB validaton report
Full document	4rls_full_validation.pdf.gz	1.8 MB	Display
Data in XML	4rls_validation.xml.gz	55.6 KB	Display
Data in CIF	4rls_validation.cif.gz	78.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rl/4rls ftp://data.pdbj.org/pub/pdb/validation_reports/rl/4rls	HTTPS FTP

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Related structure data

Similar structure data	6bb2-2 9ldt-1 4okn-2 5zjf-1 6zzr-2 4i8x-1 3h3f-2 5k0z-d 5zjd-2 5zje-3 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#102 - Jun 2008 Lactate Dehydrogenase similarity (11) #154 - Oct 2012 Citric Acid Cycle similarity (6) #142 - Oct 2011 PDB Pioneers similarity (10) #93 - Sep 2007 Citrate Synthase similarity (1)

Deposited unit

A: L-lactate dehydrogenase A chain

B: L-lactate dehydrogenase A chain

C: L-lactate dehydrogenase A chain

D: L-lactate dehydrogenase A chain

hetero molecules

150 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	77.234, 81.758, 104.563
Angle α, β, γ (deg.)	90.00, 98.28, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 4 molecules ABCD

#1: Protein	L-lactate dehydrogenase A chain / LDH-A / Cell proliferation-inducing gene 19 protein / LDH muscle subunit / LDH-M / Renal carcinoma ...LDH-A / Cell proliferation-inducing gene 19 protein / LDH muscle subunit / LDH-M / Renal carcinoma antigen NY-REN-59 Mass: 36603.473 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LDHA, PIG19 / Production host: Escherichia coli (E. coli) / References: UniProt: P00338, L-lactate dehydrogenase

#1: Protein

L-lactate dehydrogenase A chain / LDH-A / Cell proliferation-inducing gene 19 protein / LDH muscle subunit / LDH-M / Renal carcinoma ...

Mass: 36603.473 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: LDHA, PIG19 / Production host:

Escherichia coli (E. coli) / References: UniProt: P00338, L-lactate dehydrogenase

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Non-polymers , 5 types, 757 molecules

#2: Chemical	ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH Mass: 665.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₉N₇O₁₄P₂
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-2OP / (2S)-2-HYDROXYPROPANOIC ACID Mass: 90.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₆O₃
#5: Chemical	ChemComp-49C / (1R)-5'-[(2-chlorophenyl)sulfanyl]-4'-hydroxy-2,3-dihydrospiro[indene-1,2'-pyran]-6'(3'H)-one Mass: 358.839 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₉H₁₅ClO₃S
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 748 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.23 Å³/Da / Density % sol: 44.87 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: PEG3350, sodium malonate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 110 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 14, 2012
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.86→50 Å / Num. all: 95334 / Num. obs: 93076 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / B_iso Wilson estimate: 31 Å² / R_sym value: 0.045 / Net I/σ(I): 17.1

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Processing

Software

Name	Version	Classification
Blu-Ice		data collection
PHASER		phasing
REFMAC	5.8.0049	refinement
XDS		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.91→50 Å / Cor.coef. F_o:F_c: 0.953 / Cor.coef. F_o:F_c free: 0.94 / SU B: 8.579 / SU ML: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.185 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23341	1894	2 %	RANDOM
R_work	0.19157	-	-	-
all	0.21	100710	-	-
obs	0.19246	91182	92.42 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 34.684 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.92 Å²	0 Å²	-0.41 Å²
2-	-	1.12 Å²	0 Å²
3-	-	-	-0.08 Å²

Refinement step

Cycle: LAST / Resolution: 1.91→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10162	0	222	748	11132

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.019	10649
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	10547
X-RAY DIFFRACTION	r_angle_refined_deg	1.275	1.999	14459
X-RAY DIFFRACTION	r_angle_other_deg	0.765	3	24326
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.531	5	1327
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.267	25.012	403
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.491	15	1958
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.636	15	44
X-RAY DIFFRACTION	r_chiral_restr	0.068	0.2	1696
X-RAY DIFFRACTION	r_gen_planes_refined	0.015	0.02	11690
X-RAY DIFFRACTION	r_gen_planes_other	0.012	0.02	2238
X-RAY DIFFRACTION	r_mcbond_it	4.083	3.658	5261
X-RAY DIFFRACTION	r_mcbond_other	4.085	3.659	5262
X-RAY DIFFRACTION	r_mcangle_it	5.174	8.167	6567
X-RAY DIFFRACTION	r_mcangle_other	5.169	8.167	6567
X-RAY DIFFRACTION	r_scbond_it	6.758	4.795	5388
X-RAY DIFFRACTION	r_scbond_other	6.757	4.795	5389
X-RAY DIFFRACTION	r_scangle_other	8.983	10.187	7881
X-RAY DIFFRACTION	r_long_range_B_refined	9.947	11.738	12741
X-RAY DIFFRACTION	r_long_range_B_other	9.945	11.738	12741

LS refinement shell

Resolution: 1.905→2.008 Å / Total num. of bins used: 10

	R_factor	Num. reflection	% reflection
R_free	0.477	213	-
R_work	0.434	10841	-
obs	-	-	75.57 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	1.2266	0.4422	0.5304	1.3161	0.6323	0.4093	0.0084	0.054	0.0102	-0.1877	-0.0257	0.0601	-0.0504	-0.004	0.0173	0.1227	-0.0192	-0.0047	0.1199	0.0312	0.018	10.1105	-3.7758	-2.2213
2	0.3927	0.0096	0.1523	0.9886	-0.1358	0.2166	-0.0227	0.0484	-0.0026	-0.1075	0.1159	-0.0837	-0.0177	0.0387	-0.0932	0.0735	-0.0538	0.0368	0.0935	-0.0399	0.0847	27.0387	5.6388	10.92
3	2.6686	1.4562	0.8147	2.0836	0.3708	1.3517	-0.1206	0.138	-0.0685	-0.0754	0.1767	-0.2448	-0.1039	0.1512	-0.056	0.0693	-0.0575	0.038	0.0833	-0.0187	0.0854	36.6083	22.1164	12.0566
4	0.3654	0.0981	-0.1197	0.4932	-0.2292	0.7403	-0.0288	-0.0368	0.0251	-0.0295	0.0534	-0.0897	-0.03	0.074	-0.0246	0.053	-0.0274	-0.0023	0.0622	-0.0234	0.0721	29.133	19.1823	30.5265
5	0.3716	0.1443	-0.2978	1.2155	1.3587	2.57	0.0539	-0.0118	-0.0981	-0.0482	0.091	-0.1846	-0.1792	0.1448	-0.1449	0.0318	-0.0158	-0.0239	0.0965	-0.0496	0.1098	37.7413	15.2334	41.5076
6	0.9999	0.0656	0.1651	0.4933	0.0107	0.3591	-0.0645	0.0465	-0.0144	0.0265	0.1683	-0.062	-0.0091	0.0631	-0.1037	0.0735	-0.0147	0.0025	0.0887	-0.0167	0.0861	20.5148	14.1816	25.3709
7	1.0172	0.4754	-0.6874	0.5134	-0.3005	2.9154	0.0426	-0.0191	0.1717	0.0467	0.0005	-0.0613	-0.3246	-0.0116	-0.0431	0.1365	-0.0386	0.0225	0.0193	-0.0269	0.1239	33.2001	34.2795	28.0383
8	0.889	-0.2382	-0.7487	0.5498	-0.4302	1.4568	0.0417	-0.0686	0.0586	0.0384	0.0768	0.026	-0.1359	-0.0196	-0.1185	0.0996	-0.0279	0.0033	0.0575	-0.0098	0.1044	20.2145	25.6619	28.3966
9	1.2629	-0.5628	-0.4786	2.9519	1.9531	1.4661	0.085	-0.134	-0.0086	0.1585	-0.0825	-0.1111	0.0332	-0.0183	-0.0025	0.0885	0.0111	-0.0493	0.0998	0.0233	0.0471	26.0948	1.3597	53.4248
10	0.1414	-0.1803	-0.2694	1.2911	0.3776	0.8533	-0.0639	-0.08	0.0472	0.1015	0.1998	-0.2133	0.0332	0.1491	-0.1359	0.0629	0.0269	-0.0492	0.15	-0.0762	0.1371	34.7234	-5.4014	32.3075
11	4.3507	0.3506	-1.283	1.8002	0.0413	1.0856	-0.178	-0.0532	0.0806	0.0291	0.3364	-0.306	0.1636	0.2213	-0.1584	0.0322	0.0399	-0.0357	0.1646	-0.0952	0.0826	43.3452	-19.7398	27.623
12	0.7689	-0.3469	0.2399	0.4304	0.0731	0.5632	-0.0473	0.0208	0.0037	-0.0271	0.0419	-0.0398	0.0377	0.0638	0.0054	0.06	-0.009	-0.0185	0.0681	0.0022	0.0648	28.3793	-19.4345	14.2092
13	0.8619	0.3846	0.3171	1.5084	0.9295	1.0806	0.0476	0.0547	-0.0854	-0.1214	0.133	-0.1955	-0.0116	0.0954	-0.1807	0.0681	-0.0356	0.0332	0.0647	-0.039	0.0504	28.5674	-14.9153	0.4424
14	0.2846	0.5112	-0.1613	1.5773	-0.2018	0.469	0.0058	-0.0058	0.0117	-0.0013	0.1452	-0.0514	0.0164	0.0642	-0.1509	0.0599	0.005	-0.0175	0.0991	-0.0065	0.0836	22.9684	-15.7818	23.403
15	1.9062	-0.5276	1.0819	1.1853	0.5965	2.0256	0.0658	0.0536	-0.1384	-0.0116	0.0725	-0.1163	0.2703	0.1661	-0.1383	0.103	0.0239	0.0063	0.0228	-0.0236	0.074	35.5942	-33.5861	13.3687
16	0.395	0.1122	0.1435	1.0132	-0.1579	1.3099	-0.0697	-0.0262	-0.0408	-0.0374	0.0312	0.0602	0.1019	-0.0399	0.0385	0.0978	0.0077	-0.0083	0.0706	0.0007	0.0823	23.2278	-27.301	20.6392
17	1.1595	-0.4128	-0.2429	1.5842	2.3544	3.6878	-0.0879	-0.0533	-0.1397	0.1769	0.1743	0.0136	0.3038	0.2196	-0.0864	0.1324	0.0019	-0.0105	0.0466	0.0505	0.1038	16.2854	-30.6488	27.5587
18	0.3005	-0.0576	0.0595	0.1264	-0.1734	0.7617	-0.018	-0.0274	-0.0092	0.0416	0.0058	0.0588	0.1056	-0.0233	0.0123	0.0887	-0.0247	0.021	0.0896	0.0253	0.0767	3.1352	-13.4965	37.1684
19	0.4761	-0.0113	-0.3345	0.3112	0.3527	0.7097	0.096	-0.0711	-0.0582	0.1796	-0.1333	0.0359	0.1036	-0.0522	0.0373	0.1822	-0.0443	0.0642	0.1506	0.0356	0.0929	-1.4175	-9.8032	54.8842
20	0.3287	0.1784	-0.0631	1.2099	-0.2319	0.4249	-0.0259	-0.0523	0.1014	0.1009	0.0539	0.1324	0.0007	-0.0931	-0.0279	0.0549	0.0121	0.0226	0.0843	0.006	0.0544	6.6519	7.506	48.0938
21	0.7509	0.7628	0.1193	1.6109	0.3753	0.5117	0.1222	-0.0354	0.1356	0.1345	-0.0677	0.16	0.0136	-0.1417	-0.0545	0.0462	0.0246	0.029	0.0879	-0.006	0.0949	-0.4109	19.4525	44.2233
22	1.0583	-0.4783	0.1639	0.9385	0.6626	0.7832	-0.0164	0.0348	-0.0535	0.1359	0.0057	0.0495	0.1148	0.0052	0.0107	0.0891	0.0029	-0.0059	0.1157	0.0217	0.0604	13.3483	0.3279	42.4675
23	1.3636	1.509	-0.3424	2.3417	-0.0488	0.9285	0.1443	-0.1703	0.1384	0.5717	-0.0801	0.164	0.0417	-0.0125	-0.0641	0.2918	0.0407	0.0315	0.1512	-0.0255	0.0178	5.249	7.3841	63.9851
24	0.0799	0.2702	-0.1157	1.496	0.1516	0.7634	0.0409	-0.0107	0.009	0.2278	0.0222	-0.0831	0.0911	0.0025	-0.0631	0.1007	0.0145	-0.0143	0.1254	-0.0114	0.0744	16.1863	4.4374	53.2728
25	1.0258	1.4851	0.8554	2.3557	1.9251	3.8148	-0.0675	0.0443	0.0935	-0.1319	0.0831	0.1589	-0.3815	-0.0621	-0.0156	0.0716	0.0391	0.0041	0.0405	0.0328	0.1294	10.4285	27.2492	26.8682
26	0.4049	0.1964	0.164	0.2191	0.0115	0.9535	-0.0451	0.0162	0.0331	-0.0027	0.032	0.0664	-0.0826	-0.0744	0.0132	0.0552	0.02	-0.0137	0.1012	0.0142	0.079	-2.5996	7.5398	24.4412
27	0.5621	0.3841	-0.4307	3.165	-0.211	0.7976	-0.0988	0.144	0.0873	-0.0087	0.0385	0.3832	-0.0415	-0.2005	0.0604	0.0496	0.0051	-0.0364	0.1223	0.0124	0.0853	-14.7096	1.2144	12.9057
28	0.4858	-0.3146	-0.0727	0.541	-0.0089	0.4059	-0.0499	0.0064	-0.0962	-0.0139	0.0689	0.1105	0.0092	-0.0668	-0.019	0.0475	-0.0243	-0.0295	0.0706	0.0218	0.0819	-1.9739	-12.9209	12.4846
29	0.8428	-0.4377	-0.1304	1.0419	0.7181	1.2528	-0.0394	0.0456	-0.1477	0.0521	0.01	0.1643	0.171	-0.1877	0.0294	0.0924	-0.0872	-0.0033	0.0982	0.0098	0.0871	-3.3667	-26.1046	18.9187
30	0.091	0.0022	-0.2836	0.0318	0.1076	1.4718	-0.0224	-0.0387	0.0483	-0.0108	0.0175	0.0504	0.0381	0.0548	0.0049	0.0822	-0.0091	-0.0249	0.1101	0.0188	0.1058	5.4138	-4.6154	13.7915
31	3.0157	-1.4128	-0.2144	3.1604	1.0127	0.5249	-0.0032	0.3522	-0.2804	-0.1984	-0.091	0.4033	-0.0892	-0.0127	0.0942	0.064	-0.0303	-0.0661	0.1251	-0.0257	0.1187	-11.3999	-14.1607	-0.2687
32	0.535	-0.1814	0.1948	1.7943	0.2315	0.2485	0.0313	-0.0397	-0.0459	-0.1495	-0.0465	-0.0321	0.0054	-0.0215	0.0152	0.0807	-0.0231	-0.0246	0.1005	0.0092	0.0627	2.7092	-8.6789	2.9536

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 20
2	X-RAY DIFFRACTION	2	A	21 - 93
3	X-RAY DIFFRACTION	3	A	94 - 132
4	X-RAY DIFFRACTION	4	A	133 - 209
5	X-RAY DIFFRACTION	4	A	801
6	X-RAY DIFFRACTION	5	A	210 - 250
7	X-RAY DIFFRACTION	6	A	251 - 273
8	X-RAY DIFFRACTION	7	A	274 - 286
9	X-RAY DIFFRACTION	7	A	307 - 331
10	X-RAY DIFFRACTION	8	A	287 - 306
11	X-RAY DIFFRACTION	9	B	1 - 20
12	X-RAY DIFFRACTION	10	B	21 - 93
13	X-RAY DIFFRACTION	11	B	94 - 132
14	X-RAY DIFFRACTION	12	B	133 - 209
15	X-RAY DIFFRACTION	12	B	802
16	X-RAY DIFFRACTION	12	B	801
17	X-RAY DIFFRACTION	13	B	210 - 250
18	X-RAY DIFFRACTION	14	B	251 - 273
19	X-RAY DIFFRACTION	15	B	274 - 286
20	X-RAY DIFFRACTION	15	B	307 - 331
21	X-RAY DIFFRACTION	16	B	287 - 306
22	X-RAY DIFFRACTION	17	C	1 - 20
23	X-RAY DIFFRACTION	18	C	21 - 93
24	X-RAY DIFFRACTION	19	C	94 - 132
25	X-RAY DIFFRACTION	20	C	133 - 209
26	X-RAY DIFFRACTION	20	C	803
27	X-RAY DIFFRACTION	20	C	801
28	X-RAY DIFFRACTION	21	C	210 - 250
29	X-RAY DIFFRACTION	22	C	251 - 273
30	X-RAY DIFFRACTION	23	C	274 - 286
31	X-RAY DIFFRACTION	23	C	307 - 331
32	X-RAY DIFFRACTION	24	C	287 - 306
33	X-RAY DIFFRACTION	25	D	1 - 20
34	X-RAY DIFFRACTION	26	D	21 - 93
35	X-RAY DIFFRACTION	27	D	94 - 132
36	X-RAY DIFFRACTION	28	D	133 - 209
37	X-RAY DIFFRACTION	28	D	802
38	X-RAY DIFFRACTION	28	D	801
39	X-RAY DIFFRACTION	29	D	210 - 250
40	X-RAY DIFFRACTION	30	D	251 - 273
41	X-RAY DIFFRACTION	31	D	274 - 286
42	X-RAY DIFFRACTION	31	D	307 - 331
43	X-RAY DIFFRACTION	32	D	287 - 306

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